@MASTERSTHESIS{Abdu02,
  author = {Matin Abdullah},
  title = {{S}im{DB} - A Grid Software Environment for Molecular Dynamics Simulation
           and Analysis: Design and User Interface},
  school = {University of Houston},
  year = {2002},
  type = {Master's Thesis},
  month = {December}
}

@ARTICLE{Chan96,
  author = {T.~M. Chan},
  title = {Output sensitive results on convex hulls, extreme points and related problems},
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  volume = {16},
  pages = {369--387}
}

@ARTICLE{CQRS03,
  author = {Jordan H. Chill and Sabine R. Quadt and Rina Levy and Gideon Schreiber and Jacob Anglister},
  title = {The Human Type I Interferon Receptor: {NMR} Structure Reveals the Molecular Basis of Ligand Binding},
  journal = {Structure},
  year = {2003},
  volume = {11},
  number = {7},
  pages = {791--802},
  url = {http://www.sciencedirect.com/science/article/B6VSR-490H19R-9/2/fe5e56683ffb64b44b94f2471ef92e3b}
}

@ARTICLE{DobK99,
  author = {Christopher M Dobson and Martin Karplus},
  title = {The fundamentals of protein folding: bringing together theory and experiment},
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  volume = {9},
  number = {1},
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  url = {http://www.sciencedirect.com/science/article/B6VS6-3W8SDFR-D/2/263f32510d9791b5366edcd70c01b6e3}
}

@MISC{FoldatHome, 
    author       = {Vijay S. Pande},
    title        = {Folding@home},
    howpublished = {\url{http://www.stanford.edu/group/pandegroup/folding/}},
    month        = JUL,
    year         = {2004},
    annote       = {},
    README       = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{HDOF98,
  author = {Hilser, Vincent and Dowdy, David and Oas, Terrence and Freire, Ernesto},
  title = {The structural distribution of cooperative interactions in proteins:
      Analysis of the native state ensemble},
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  year = {1998},
  volume = {95},
  pages = {9903-9908}
}

@ARTICLE{HGHW92,
  author = {S. G. Hyberts and M. S. Goldberg and T. F. Havel and G. Wagner},
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  year = {1992},
  volume = {1},
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}

@ARTICLE{IsLT01,
  author = {Ishima, Rieko and Louis, John and Torchia, Dennis},
  title = {Characterization of Two Hydrophobic Methyl Clusters in {HIV}-1
      Protease by {NMR} Spin Relaxation in Solution},
  journal = {J. Mol. Biol.},
  year = {2001}
}

@ARTICLE{JiKi91,
  author = {F. Jiang and S. H. Kim},
  title = {``{S}oft {D}ocking'': Matching of molecular surface cubes},
  journal = JMB,
  year = {1991},
  volume = {219},
  pages = {79--102},
}

@ARTICLE{Jose99,
  author = {Diane Joseph-McCarthy},
  title = {Computational approaches to structure-based ligand design},
  journal = {Pharmacology \& Therapeutics},
  year = {1999},
  volume = {84},
  number = {2},
  pages = {179--191},
  url = {http://www.sciencedirect.com/science/article/B6TBG-3XP7FKT-5/2/4b2019f9a2992c0c9dd2d1e3f5cdb732}
}

@ARTICLE{JRKT01,
  author = {Donald Jacobs and A. J. Rader and Leslie Kuhn and M. F. Thorpe},
  title = {Protein Flexibility Predictions Using Graph Theory},
  journal = PRO,
  year = {2001},
  volume = {44},
  pages = {150--165}
}

@ARTICLE{KLLT00,
  author = {P. A. Keller and S. P. Leach and T. T. Luu and S. J. Titmuss and R. Griffith},
  title = {Development of computational and graphical tools for the analysis of
          movement and flexibility of large molecules},
  journal = JMGM,
  year = {2000}
}

@ARTICLE{Leac94,
  author = {Andrew R. Leach},
  title = {Ligand docking to proteins with discrete side-chain flexibility},
  journal = JMB,
  year = {1994},
  volume = {235},
  pages = {345--356}
}

@ARTICLE{LuqF00,
  author = {Irene Luque and Ernesto Freire},
  title = {Structural Stability of Binding Sites: Consequences for Binding
      Affinity and Allosteric Effects},
  journal = PRO,
  year = {2000},
  volume = {4},
  pages = {63--71}
}

@ARTICLE{MaiA97,
  author = {V. Maiorov and R. Abagyan},
  title = {A new method for modeling large-scale rearrangements of protein domains},
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  year = {1997},
  volume = {27},
  pages = {410--424},
}

@MISC{MMOS,
    author       = {MMOS},
    title        = {Molecular Mechanics Open Standards - Working Group},
    howpublished =
    {\url{http://dirac.cnrs-orleans.fr/fsatom_wiki/MolecularMechanicsOpenStandards/}},
    month        = JUL,
    year         = {2004},
    annote       = {Molecular Mechanics Markup Language. Free Software for Atomic Scale
                    Simulations Group},
    README       = {Requires \usepackage{url} in the preamble.}
}

@ARTICLE{MSWN02,
  author = {B. Ma and M. Shatsky and J. Wolfson and R. Nussinov},
  title = {Multiple diverse ligands binding at a single protein site: {A} matter
      of pre-existing populations.},
  journal = {Protein Science},
  year = {2002}
}

@ARTICLE{PeMA04,
  author = {Jeffrey W. Peng and Jonathan Moore and Norzehan Abdul-Manan},
  title = {{NMR} experiments for lead generation in drug discovery},
  journal = {Progress in Nuclear Magnetic Resonance Spectroscopy},
  year = {2004},
  volume = {44},
  number = {3-4},
  pages = {225--256},
  www = {http://www.sciencedirect.com/science/article/B6THC-4CDJWP6-1/2/638a7627a8767b40f1203b8b44462ab5}
}

@ARTICLE{PhLi99,
  author = {Marios Philippopoulos and Carmay Lim},
  title = {Exploring the Dynamic Information Content of a Protein {NRM} Structure:
      Comparison of a Molecular Dynamics Simulation with the {NMR} and {X}-Ray
              Structures of {E}scherichia {C}oli Ribonuclease {HI}},
  journal = PRO,
  year = {1999},
  volume = {36},
  pages = {87-110},
  pdf = {Papers/PhiL99.pdf},
}

@ARTICLE{RadS04,
  author = {Ravi Radhakrishnan and Tamar Schlick},
  title = {Orchestration of cooperative events in {DNA} synthesis and repair
           mechanism unraveled by transition path sampling of {DNA} polymerase
           $\beta$'s closing},
  journal = {PNAS},
  year = {2004},
  volume = {101},
  number = {16},
  pages = {5970-5975}
}

@ARTICLE{SchV98,
  author = {L. Schaffer and G. M. Verkhivker},
  title = {Predicting structural effects in {HIV}-1 protease mutant complexes with flexible ligand docking},
  journal = {Proteins},
  year = {1998},
  volume = {33},
  pages = {295-310}
}

@ARTICLE{SHWG94,
  author = {Celia A. Schiffer and Robert Huber and Kurt Wuthrich and Wilfred F. van Gunsteren},
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      Measured in Solution and {X}-ray Diffraction Data Measured in Single
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  journal = JMB,
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}

@MISC{SimDB,
    author       = {Lienert Johnson and B. Montgomery Pettitt},
    title        = {{S}im{DB}},
    howpublished = {\url{http://www2.cs.uh.edu/~mdtdb/}},
    month        = JUL,
    year         = {2004},
    README       = {Requires \usepackage{url} in the preamble.}
}


@ARTICLE{SmDV02,
  author = {Smith, Lorna and Daura, Xavier and van Gunsteren, Wilfred},
  title = {Assessing Equilibration and Convergence in Biomolecular Simulations},
  journal = PROTEINS,
  year = {2002},
  volume = {48},
  pages = {487-496}
}

@ARTICLE{VBGR02,
  author = {Gennady M. Verkhivker and Djamal Bouzida and Daniel K. Gehlhaar and
      Paul A. Rejto and Stephan T. Freer and Peter W. Rose},
  title = {Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective},
  journal = {Current Opinion in Structural Biology},
  year = {2002},
  volume = {12},
  number = {2},
  pages = {197--203},
  url = {http://www.sciencedirect.com/science/article/B6VS6-45JPC7V-C/2/a64f67f80831c6e628f2a966690db9af}
}

@ARTICLE{WriS97,
  author = {Wriggers, W and Schulten, K},
  title = {Protein domain movements: Detection of rigid domains and visualization of hinges in comparison of atomic coordinates },
  journal = {Proteins},
  year = {1997},
  volume = {29},
  pages = {1-14},
}

@ARTICLE{ZacS99,
  author = {Zacharias, M and Sklenar, N},
  title = {Harmonic modes as variables to approximately account for receptor
      flexibility in ligand-receptor docking simulations: Applications to {DNA}
      minor groove ligand complex},
  journal = JCC,
  year = {1999},
  volume = {20},
  pages = {287-300},
}


@BOOK{BKOS00,
  author = {M. de Berg and M. van Krevald and M. Overmars and O. Schwarzkopf},
  title = {Computational {G}eometry: {A}lgorithms and {A}pplications},
  year = {2000},
  publisher = {Springer},
  edition = {2nd},
}

@ARTICLE{IsTo00,
  author = {Rieko Ishima and Dennis A.~Torchia},
  title = {Protein dynamics from {NMR}},
  journal = NATSB,
  year = {2000},
  volume = {7},
  pages = {740--743},
}

@ARTICLE{IsTo99,
    author  = {Rieko Ishima and Dennis A.~Torchia},
    title   = {Estimating the time scale of chemical exchange of proteins from
               measurements of transverse relaxation rates in solution},
    journal = JBNMR,
    year    = {1999},
    month   = AUG,
    volume  = {14},
    number  = {4},
    pages   = {369--372}
}

@ARTICLE{Verk01,
    author  = {Gennady M. Verkhivker and Paul A. Rejto and Djamal Bouzida and
               Sandra Arthurs and Anthony B. Colson and Stephan T. Freer and
               Daniel K. Gehlhaar and Veda Larson and Brock A. Luty and Tami
               Marrone and Peter W. Rose},
    title   = {Parallel simulated tempering dynamics of ligand-protein binding
               with ensembles of protein conformations},
    journal = CPL,
    year    = {2001},
    month   = MAR,
    volume  = {337},
    pages   = {181--189}
}

@ARTICLE{Carl00,
    author  = {Heather A. Carlson and Kevin M. Masukawa and Kathleen Rubins and
               Fredric D. Bushman and William L. Jorgensen and Roberto D. Lins
               and James M. Briggs and J. Andrew McCammon},
    title   = {Developing a Dynamic Pharmacophore Model for {HIV}-1 Integrase},
    journal = JMC,
    year    = {2000},
    volume  = {43},
    number  = {11},
    pages   = {2100--2114}
}

@MISC{DOCK,
    author       = {{DOCK}},
    howpublished = {\url{http://dock.compbio.ucsf.edu/}},
    month        = JUL,
    year         = {2004},
    README       = {Requires \usepackage{url} in the preamble.}
}

@MISC{FLEXE,
    author       = {{FLEXE}},
    howpublished = {\url{http://www.biosolveit.de/software/}},
    month        = JUL,
    year         = {2004},
    README       = {Requires \usepackage{url} in the preamble.}
}

@MISC{AUTODOCK,
    author       = {{AUTODOCK}},
    title        = {Automated docking of flexible ligands to macromolecules},
    howpublished = {\url{http://www.scripps.edu/pub/olson-web/doc/autodock/}},
    month        = JUL,
    year         = {2004},
    README       = {Requires \usepackage{url} in the preamble.}
}

@MISC{CAPRI,
    author       = {CAPRI},
    title        = {Critical {A}ssessment of {PR}ediction of {I}nteractions},
    howpublished = {\url{http://capri.ebi.ac.uk/}},
    month        = JUL,
    year         = {2004},
    README       = {Requires \usepackage{url} in the preamble.}
}

@MISC{OGCE,
    author       = {OGCE},
    title        = {Open {G}rid {C}omputing {E}nvironments},
    howpublished = {\url{http://www.collab-ogce.org/nmi/index.jsp}},
    month        = JUL,
    year         = {2004},
    README       = {Requires \usepackage{url} in the preamble.}
}


@ARTICLE{AbaT01,
    author  = {Abagyan, R and Totrov, M},
    title   = {High-throughput docking for lead generation},
    journal = COCHB,
    year    = {2001},
    volume  = {5},
    pages   = {375--382}
}

@ARTICLE{TavG02,
    author  = {Taverna, DM and Goldstein, RA},
    title   = {Why are proteins marginally stable?},
    journal = PSFG,
    year    = {2002},
    volume  = {46},
    pages   = {105--109}
}
@ARTICLE{KPCH00,
    author  = {Kastenholz, MA and Pastor, M and Cruciani, G and
             Haaksma, EEJ and Fox, T},  
    title   = {GRID/CPCA: A new computational tool to design selective ligand},
    journal = JMC,
    year    = {2000},
    volume  = {43},
    pages   = {3033--3044}
}
@ARTICLE{KnKO97,
    author  = {Knegtel, RMA and Kuntz, ID and Oshiro, CM},
    title   = {Molecular docking to ensembles of protein structure},
    journal = JMB,
    year    = {1997},
    volume  = {266},
    pages   = {424--440}
}

@BOOK{WNDS01,
    author = "M. Woo and J. Neider and T. Davis and D. Shreiner",
    title = "Modeling Transformations",
    book = "{OpenGL} Programming Guide",
    pages = "110-118",
    year = "2001" }

@BOOK{Ange00,
    author = "E. Angel",
    chapter = "Rotation, Translation, and Scaling",
    booktitle = "Interactive Computer Graphics",
    pages = "163-178",
    year = "2000" }